Last updated on 2020-02-19 10:48:46 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.0 | 2.82 | 29.73 | 32.55 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.0.0 | 3.08 | 23.30 | 26.38 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.0.0 | 40.28 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.0 | 39.20 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 2.0.0 | 13.00 | 54.00 | 67.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 2.0.0 | 20.00 | 73.00 | 93.00 | OK | |
| r-patched-linux-x86_64 | 2.0.0 | 2.70 | 38.54 | 41.24 | OK | |
| r-patched-solaris-x86 | 2.0.0 | 75.00 | OK | |||
| r-release-linux-x86_64 | 2.0.0 | 3.00 | 39.71 | 42.71 | OK | |
| r-release-windows-ix86+x86_64 | 2.0.0 | 10.00 | 54.00 | 64.00 | OK | |
| r-release-osx-x86_64 | 2.0.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 2.0.0 | 6.00 | 50.00 | 56.00 | OK | |
| r-oldrel-osx-x86_64 | 2.0.0 | OK |
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in 'AssayCorrector-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: correct_bias
> ### Title: Correct the bias present in the assay, previously detected by
> ### the 'detect_bias()' method
> ### Aliases: correct_bias
>
> ### ** Examples
>
> assay<-create_assay(m)
> detected<-detect_bias(assay)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
AssayCorrector
--- call from context ---
detect_bias(assay)
--- call from argument ---
if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem")
--- R stacktrace ---
where 1: detect_bias(assay)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (assay, alpha = 0.01, type = "P", test = "AD")
{
if (class(assay) != "assay")
stop("Error: This is not an assay.")
ac = as.character
m = assay$m
ctrl = assay$ctrl
biasType = assay$biasType
biasModel = assay$biasModel
biasConf = assay$biasConf
PMPmapping = c(1, 4, 5, 3, 2, 6)
m.E <- new.env()
for (model in 1:6) {
m.E[[ac(model)]] = ctrl
}
dimensions = dim(m)
Depth = dimensions[3]
.test.f = NULL
if (test == "KS")
.test.f = function(x, y) ks.test(x, y)$p.value
else if (test == "AD")
.test.f = function(x, y) as.numeric(tail(strsplit(capture.output(kSamples::ad.test(x,
y))[17], " ")[[1]], 1))
else if (test == "CVM")
.test.f = function(x, y) RVAideMemoire::CvM.test(x, y)$p.value
else {
stop("Error: This is not a valid test. Please use KS, AD or CVM")
}
if (type == "AP")
m = .assay(m, ctrl, alpha)
for (k in 1:Depth) {
for (model in 1:6) {
m.E[[ac(model)]][, , k] = try(.PMP(m[, , k], ctrl[,
, k], PMPmapping[model], alpha))
if (class(m.E[[ac(model)]][, , k]) == "try-error")
stop("PMP encountered a problem")
}
mww = (m.E[[ac(1)]][, , k] != m[, , k]) * 1
assay$biasPositions[, , k] = mww
biased.E = new.env()
unbiased = list()
for (i in 1:dimensions[1]) {
for (j in 1:dimensions[2]) {
if (mww[i, j] & !ctrl[i, j, k]) {
for (model in 1:6) {
biased.E[[ac(model)]] = c(biased.E[[ac(model)]],
m.E[[ac(model)]][i, j, k])
}
}
else if (!mww[i, j] & !ctrl[i, j, k])
unbiased = c(unbiased, m.E[[ac(model)]][i,
j, k])
}
}
for (model in 1:6) {
biased.E[[ac(model)]] = unlist(biased.E[[ac(model)]])
}
unbiased = unlist(unbiased)
if (Reduce(function(x, y) length(biased.E[[ac(y)]]) *
x, 1:6, 1) == 0) {
biasType[k] = "C"
next
}
pvalue.E = new.env()
for (model in 1:6) {
pvalue.E[[ac(model)]] = .test.f(biased.E[[ac(model)]],
unbiased)
}
aMethods = 1:3
mMethods = 4:6
p = function(model) pvalue.E[[ac(model)]]
if (all(sapply(aMethods, p) < alpha) & any(sapply(mMethods,
p) > alpha)) {
biasType[k] = "M"
biasModel[k] = 3 + which.max(sapply(mMethods, p))
biasConf[k] = sum(sapply(mMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & any(sapply(aMethods,
p) > alpha)) {
biasType[k] = "A"
biasModel[k] = which.max(sapply(aMethods, p))
biasConf[k] = sum(sapply(aMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & all(sapply(aMethods,
p) < alpha)) {
biasType[k] = "U"
}
else if (all(sapply(mMethods, p) > alpha) & all(sapply(aMethods,
p) > alpha)) {
biasModel[k] = which.max(sapply(c(aMethods, mMethods),
p))
biasConf[k] = sum(sapply(c(aMethods, mMethods), p) >
alpha)
biasType[k] = ifelse(biasModel[k] %in% aMethods,
"A", "M")
}
else {
biasType[k] = "U"
}
}
assay$biasType = biasType
assay$biasModel = biasModel
assay$biasConf = biasConf
return(assay)
}
<bytecode: 0x2689180>
<environment: namespace:AssayCorrector>
--- function search by body ---
Function detect_bias in namespace AssayCorrector has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem") :
the condition has length > 1
Calls: detect_bias
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in ‘AssayCorrector-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: correct_bias
> ### Title: Correct the bias present in the assay, previously detected by
> ### the 'detect_bias()' method
> ### Aliases: correct_bias
>
> ### ** Examples
>
> assay<-create_assay(m)
> detected<-detect_bias(assay)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
AssayCorrector
--- call from context ---
detect_bias(assay)
--- call from argument ---
if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem")
--- R stacktrace ---
where 1: detect_bias(assay)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (assay, alpha = 0.01, type = "P", test = "AD")
{
if (class(assay) != "assay")
stop("Error: This is not an assay.")
ac = as.character
m = assay$m
ctrl = assay$ctrl
biasType = assay$biasType
biasModel = assay$biasModel
biasConf = assay$biasConf
PMPmapping = c(1, 4, 5, 3, 2, 6)
m.E <- new.env()
for (model in 1:6) {
m.E[[ac(model)]] = ctrl
}
dimensions = dim(m)
Depth = dimensions[3]
.test.f = NULL
if (test == "KS")
.test.f = function(x, y) ks.test(x, y)$p.value
else if (test == "AD")
.test.f = function(x, y) as.numeric(tail(strsplit(capture.output(kSamples::ad.test(x,
y))[17], " ")[[1]], 1))
else if (test == "CVM")
.test.f = function(x, y) RVAideMemoire::CvM.test(x, y)$p.value
else {
stop("Error: This is not a valid test. Please use KS, AD or CVM")
}
if (type == "AP")
m = .assay(m, ctrl, alpha)
for (k in 1:Depth) {
for (model in 1:6) {
m.E[[ac(model)]][, , k] = try(.PMP(m[, , k], ctrl[,
, k], PMPmapping[model], alpha))
if (class(m.E[[ac(model)]][, , k]) == "try-error")
stop("PMP encountered a problem")
}
mww = (m.E[[ac(1)]][, , k] != m[, , k]) * 1
assay$biasPositions[, , k] = mww
biased.E = new.env()
unbiased = list()
for (i in 1:dimensions[1]) {
for (j in 1:dimensions[2]) {
if (mww[i, j] & !ctrl[i, j, k]) {
for (model in 1:6) {
biased.E[[ac(model)]] = c(biased.E[[ac(model)]],
m.E[[ac(model)]][i, j, k])
}
}
else if (!mww[i, j] & !ctrl[i, j, k])
unbiased = c(unbiased, m.E[[ac(model)]][i,
j, k])
}
}
for (model in 1:6) {
biased.E[[ac(model)]] = unlist(biased.E[[ac(model)]])
}
unbiased = unlist(unbiased)
if (Reduce(function(x, y) length(biased.E[[ac(y)]]) *
x, 1:6, 1) == 0) {
biasType[k] = "C"
next
}
pvalue.E = new.env()
for (model in 1:6) {
pvalue.E[[ac(model)]] = .test.f(biased.E[[ac(model)]],
unbiased)
}
aMethods = 1:3
mMethods = 4:6
p = function(model) pvalue.E[[ac(model)]]
if (all(sapply(aMethods, p) < alpha) & any(sapply(mMethods,
p) > alpha)) {
biasType[k] = "M"
biasModel[k] = 3 + which.max(sapply(mMethods, p))
biasConf[k] = sum(sapply(mMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & any(sapply(aMethods,
p) > alpha)) {
biasType[k] = "A"
biasModel[k] = which.max(sapply(aMethods, p))
biasConf[k] = sum(sapply(aMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & all(sapply(aMethods,
p) < alpha)) {
biasType[k] = "U"
}
else if (all(sapply(mMethods, p) > alpha) & all(sapply(aMethods,
p) > alpha)) {
biasModel[k] = which.max(sapply(c(aMethods, mMethods),
p))
biasConf[k] = sum(sapply(c(aMethods, mMethods), p) >
alpha)
biasType[k] = ifelse(biasModel[k] %in% aMethods,
"A", "M")
}
else {
biasType[k] = "U"
}
}
assay$biasType = biasType
assay$biasModel = biasModel
assay$biasConf = biasConf
return(assay)
}
<bytecode: 0x55d0f5716480>
<environment: namespace:AssayCorrector>
--- function search by body ---
Function detect_bias in namespace AssayCorrector has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem") :
the condition has length > 1
Calls: detect_bias
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in ‘AssayCorrector-Ex.R’ failed
The error most likely occurred in:
> ### Name: correct_bias
> ### Title: Correct the bias present in the assay, previously detected by
> ### the 'detect_bias()' method
> ### Aliases: correct_bias
>
> ### ** Examples
>
> assay<-create_assay(m)
> detected<-detect_bias(assay)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
AssayCorrector
--- call from context ---
detect_bias(assay)
--- call from argument ---
if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem")
--- R stacktrace ---
where 1: detect_bias(assay)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (assay, alpha = 0.01, type = "P", test = "AD")
{
if (class(assay) != "assay")
stop("Error: This is not an assay.")
ac = as.character
m = assay$m
ctrl = assay$ctrl
biasType = assay$biasType
biasModel = assay$biasModel
biasConf = assay$biasConf
PMPmapping = c(1, 4, 5, 3, 2, 6)
m.E <- new.env()
for (model in 1:6) {
m.E[[ac(model)]] = ctrl
}
dimensions = dim(m)
Depth = dimensions[3]
.test.f = NULL
if (test == "KS")
.test.f = function(x, y) ks.test(x, y)$p.value
else if (test == "AD")
.test.f = function(x, y) as.numeric(tail(strsplit(capture.output(kSamples::ad.test(x,
y))[17], " ")[[1]], 1))
else if (test == "CVM")
.test.f = function(x, y) RVAideMemoire::CvM.test(x, y)$p.value
else {
stop("Error: This is not a valid test. Please use KS, AD or CVM")
}
if (type == "AP")
m = .assay(m, ctrl, alpha)
for (k in 1:Depth) {
for (model in 1:6) {
m.E[[ac(model)]][, , k] = try(.PMP(m[, , k], ctrl[,
, k], PMPmapping[model], alpha))
if (class(m.E[[ac(model)]][, , k]) == "try-error")
stop("PMP encountered a problem")
}
mww = (m.E[[ac(1)]][, , k] != m[, , k]) * 1
assay$biasPositions[, , k] = mww
biased.E = new.env()
unbiased = list()
for (i in 1:dimensions[1]) {
for (j in 1:dimensions[2]) {
if (mww[i, j] & !ctrl[i, j, k]) {
for (model in 1:6) {
biased.E[[ac(model)]] = c(biased.E[[ac(model)]],
m.E[[ac(model)]][i, j, k])
}
}
else if (!mww[i, j] & !ctrl[i, j, k])
unbiased = c(unbiased, m.E[[ac(model)]][i,
j, k])
}
}
for (model in 1:6) {
biased.E[[ac(model)]] = unlist(biased.E[[ac(model)]])
}
unbiased = unlist(unbiased)
if (Reduce(function(x, y) length(biased.E[[ac(y)]]) *
x, 1:6, 1) == 0) {
biasType[k] = "C"
next
}
pvalue.E = new.env()
for (model in 1:6) {
pvalue.E[[ac(model)]] = .test.f(biased.E[[ac(model)]],
unbiased)
}
aMethods = 1:3
mMethods = 4:6
p = function(model) pvalue.E[[ac(model)]]
if (all(sapply(aMethods, p) < alpha) & any(sapply(mMethods,
p) > alpha)) {
biasType[k] = "M"
biasModel[k] = 3 + which.max(sapply(mMethods, p))
biasConf[k] = sum(sapply(mMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & any(sapply(aMethods,
p) > alpha)) {
biasType[k] = "A"
biasModel[k] = which.max(sapply(aMethods, p))
biasConf[k] = sum(sapply(aMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & all(sapply(aMethods,
p) < alpha)) {
biasType[k] = "U"
}
else if (all(sapply(mMethods, p) > alpha) & all(sapply(aMethods,
p) > alpha)) {
biasModel[k] = which.max(sapply(c(aMethods, mMethods),
p))
biasConf[k] = sum(sapply(c(aMethods, mMethods), p) >
alpha)
biasType[k] = ifelse(biasModel[k] %in% aMethods,
"A", "M")
}
else {
biasType[k] = "U"
}
}
assay$biasType = biasType
assay$biasModel = biasModel
assay$biasConf = biasConf
return(assay)
}
<bytecode: 0x3149910>
<environment: namespace:AssayCorrector>
--- function search by body ---
Function detect_bias in namespace AssayCorrector has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem") :
the condition has length > 1
Calls: detect_bias
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.0.0
Check: examples
Result: ERROR
Running examples in ‘AssayCorrector-Ex.R’ failed
The error most likely occurred in:
> ### Name: correct_bias
> ### Title: Correct the bias present in the assay, previously detected by
> ### the 'detect_bias()' method
> ### Aliases: correct_bias
>
> ### ** Examples
>
> assay<-create_assay(m)
> detected<-detect_bias(assay)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
AssayCorrector
--- call from context ---
detect_bias(assay)
--- call from argument ---
if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem")
--- R stacktrace ---
where 1: detect_bias(assay)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (assay, alpha = 0.01, type = "P", test = "AD")
{
if (class(assay) != "assay")
stop("Error: This is not an assay.")
ac = as.character
m = assay$m
ctrl = assay$ctrl
biasType = assay$biasType
biasModel = assay$biasModel
biasConf = assay$biasConf
PMPmapping = c(1, 4, 5, 3, 2, 6)
m.E <- new.env()
for (model in 1:6) {
m.E[[ac(model)]] = ctrl
}
dimensions = dim(m)
Depth = dimensions[3]
.test.f = NULL
if (test == "KS")
.test.f = function(x, y) ks.test(x, y)$p.value
else if (test == "AD")
.test.f = function(x, y) as.numeric(tail(strsplit(capture.output(kSamples::ad.test(x,
y))[17], " ")[[1]], 1))
else if (test == "CVM")
.test.f = function(x, y) RVAideMemoire::CvM.test(x, y)$p.value
else {
stop("Error: This is not a valid test. Please use KS, AD or CVM")
}
if (type == "AP")
m = .assay(m, ctrl, alpha)
for (k in 1:Depth) {
for (model in 1:6) {
m.E[[ac(model)]][, , k] = try(.PMP(m[, , k], ctrl[,
, k], PMPmapping[model], alpha))
if (class(m.E[[ac(model)]][, , k]) == "try-error")
stop("PMP encountered a problem")
}
mww = (m.E[[ac(1)]][, , k] != m[, , k]) * 1
assay$biasPositions[, , k] = mww
biased.E = new.env()
unbiased = list()
for (i in 1:dimensions[1]) {
for (j in 1:dimensions[2]) {
if (mww[i, j] & !ctrl[i, j, k]) {
for (model in 1:6) {
biased.E[[ac(model)]] = c(biased.E[[ac(model)]],
m.E[[ac(model)]][i, j, k])
}
}
else if (!mww[i, j] & !ctrl[i, j, k])
unbiased = c(unbiased, m.E[[ac(model)]][i,
j, k])
}
}
for (model in 1:6) {
biased.E[[ac(model)]] = unlist(biased.E[[ac(model)]])
}
unbiased = unlist(unbiased)
if (Reduce(function(x, y) length(biased.E[[ac(y)]]) *
x, 1:6, 1) == 0) {
biasType[k] = "C"
next
}
pvalue.E = new.env()
for (model in 1:6) {
pvalue.E[[ac(model)]] = .test.f(biased.E[[ac(model)]],
unbiased)
}
aMethods = 1:3
mMethods = 4:6
p = function(model) pvalue.E[[ac(model)]]
if (all(sapply(aMethods, p) < alpha) & any(sapply(mMethods,
p) > alpha)) {
biasType[k] = "M"
biasModel[k] = 3 + which.max(sapply(mMethods, p))
biasConf[k] = sum(sapply(mMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & any(sapply(aMethods,
p) > alpha)) {
biasType[k] = "A"
biasModel[k] = which.max(sapply(aMethods, p))
biasConf[k] = sum(sapply(aMethods, p) > alpha)
}
else if (all(sapply(mMethods, p) < alpha) & all(sapply(aMethods,
p) < alpha)) {
biasType[k] = "U"
}
else if (all(sapply(mMethods, p) > alpha) & all(sapply(aMethods,
p) > alpha)) {
biasModel[k] = which.max(sapply(c(aMethods, mMethods),
p))
biasConf[k] = sum(sapply(c(aMethods, mMethods), p) >
alpha)
biasType[k] = ifelse(biasModel[k] %in% aMethods,
"A", "M")
}
else {
biasType[k] = "U"
}
}
assay$biasType = biasType
assay$biasModel = biasModel
assay$biasConf = biasConf
return(assay)
}
<bytecode: 0x2a902c0>
<environment: namespace:AssayCorrector>
--- function search by body ---
Function detect_bias in namespace AssayCorrector has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(m.E[[ac(model)]][, , k]) == "try-error") stop("PMP encountered a problem") :
the condition has length > 1
Calls: detect_bias
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc